The seed and full alignments, accompanied by annotation and cross-references to other family and structure databases and to the literature and the HMMs, are what make up Pfam-A. Each family has a permanent accession number and can thus be referenced from other databases. For release , we strived to include every family with more than 50 members in Pfam-A. All sequence domains not in Pfam-A were then clustered and aligned automati- cally by the Domainer program into Pfam-B. To- gether, Pfam-A and Pfam-B provide a complete clus- tering of all protein sequences. The quality of the Pfam-B alignments is generally not sufficient to construct useful HMMs. The main purposes of Pfam-B are instead to.
